BACKGROUND: Parkinson's disease is the primary degenerative disease characterized by rigidity, bradykinesia and resting tremor. Even though dopaminergic cell loss of the substantia nigra compacta is a main pathogenesis of the Parkinson's disease, the striatal dysfuntion is major pathophysiology of pakinsonian symptoms. METHODS: Since gene expression profile can explain the symptomatic varieties of Parkinson's disease, gene expression was investigated in the striatum of rat brain after lesioning of unilateral substantia nigra compacta with 6-hydroxydopamine using cDNA microarray technique for the first time. The expression patterns of 5,200 rat brain cDNAs were screened and clustered according to the function of gene. The expression patterns of enkephaline and substance-P mRNA were also studied for validation of animal preparation. RESULTS: Various genes involved in apoptosis, cytokines. cytoskeletal molecules, neurotrophic factors, receptors, intracellular Ca2+ metabolism, signal transduction, stress protein, cell cycle regulator protein, and expressed sequence tags(EST) have shown significant expression changes. CONCLUSIONS: These gene expressions provide the global assessment of the processes involved in secondary change of striatum afforded by dopaminergic denervation at molecular levels.